dbSNP rs11592052: CCDC7:c.873-6107G>A (chr10-32511838-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001395015.1(CCDC7):c.873-6107G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.413 in 748,288 control chromosomes in the GnomAD database, including 71,298 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.34 ( 11478 hom., cov: 33)

Exomes 𝑓: 0.43 ( 59820 hom. )

Consequence

CCDC7
NM_001395015.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.411

Publications

3 publications found

Variant links:

Genes affected

CCDC7 (HGNC:26533): (coiled-coil domain containing 7)

CCDC7 links:

C1DP1 (HGNC:31465): (C1D nuclear receptor corepressor pseudogene 1)

C1DP1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001395015.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CCDC7	NM_001395015.1	MANE Select	c.873-6107G>A	intron	N/A	NP_001381944.1	Q96M83-1
CCDC7	NM_001321115.2		c.873-6107G>A	intron	N/A	NP_001308044.1	Q96M83-1
CCDC7	NM_001395233.1		c.478-31462G>A	intron	N/A	NP_001382162.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CCDC7	ENST00000639629.2	TSL:5 MANE Select	c.873-6107G>A	intron	N/A	ENSP00000491655.1	Q96M83-1
CCDC7	ENST00000277657.12	TSL:1	c.873-6107G>A	intron	N/A	ENSP00000277657.6	Q96M83-3
CCDC7	ENST00000362006.11	TSL:1	c.873-6107G>A	intron	N/A	ENSP00000355078.5	Q96M83-3

Frequencies

GnomAD3 genomes

AF:

0.345

AC:

52479

AN:

152078

Hom.:

11475

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0951

Gnomad AMI

AF:

0.339

Gnomad AMR

AF:

0.325

Gnomad ASJ

AF:

0.459

Gnomad EAS

AF:

0.0879

Gnomad SAS

AF:

0.312

Gnomad FIN

AF:

0.484

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.496

Gnomad OTH

AF:

0.361

GnomAD4 exome

AF:

0.431

AC:

256695

AN:

596092

Hom.:

59820

Cov.:

AF XY:

0.429

AC XY:

135260

AN XY:

314944

show subpopulations

African (AFR)

AF:

0.0928

AC:

1468

AN:

15816

American (AMR)

AF:

0.355

AC:

10629

AN:

29952

Ashkenazi Jewish (ASJ)

AF:

0.471

AC:

8406

AN:

17842

East Asian (EAS)

AF:

0.100

AC:

3221

AN:

32214

South Asian (SAS)

AF:

0.335

AC:

19064

AN:

56910

European-Finnish (FIN)

AF:

0.496

AC:

23504

AN:

47364

Middle Eastern (MID)

AF:

0.356

AC:

846

AN:

2376

European-Non Finnish (NFE)

AF:

0.488

AC:

176947

AN:

362246

Other (OTH)

AF:

0.402

AC:

12610

AN:

31372

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

7441

14883

22324

29766

37207

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1708

3416

5124

6832

8540

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.345

AC:

52482

AN:

152196

Hom.:

11478

Cov.:

AF XY:

0.341

AC XY:

25408

AN XY:

74406

show subpopulations

African (AFR)

AF:

0.0948

AC:

3938

AN:

41528

American (AMR)

AF:

0.326

AC:

4980

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.459

AC:

1594

AN:

3472

East Asian (EAS)

AF:

0.0881

AC:

458

AN:

5196

South Asian (SAS)

AF:

0.312

AC:

1505

AN:

4820

European-Finnish (FIN)

AF:

0.484

AC:

5124

AN:

10582

Middle Eastern (MID)

AF:

0.344

AC:

101

AN:

294

European-Non Finnish (NFE)

AF:

0.496

AC:

33709

AN:

67984

Other (OTH)

AF:

0.361

AC:

764

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.494

Heterozygous variant carriers

1520

3040

4560

6080

7600

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

504

1008

1512

2016

2520

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.309

Hom.:

1205

Bravo

AF:

0.322

Asia WGS

AF:

0.193

AC:

671

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

5.3

(source)

DANN

Benign

0.83

PhyloP100

0.41

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over